I noticed my twenty twelve theme is including outdated versions of jquery and js so I want to replace the scripts with the newer versions, however the scripts are in the file included by wp_head() (which I think is in wp-includes) so adding the scripts to my header means jquery will be loaded twice, I see now way to remove the scripts from wp_head() without messing with wp-include and any changes I do will probably be lost if I update wordpress.
So how can I remove the scripts from wp_head() permanently?